Hi,
A newbie to Galaxy (and computational biology) here, but seem to have acquired the role of head of blame for all things galaxy related at our site.
Are there any documentation that can give some insight on how installation of the various available packages work?
Yes,I know in general you go to Admin, click on Add a tool and follow the instructions. I am looking for info on troubleshooting strategies when the process did not work as expected.
Regards
Michael
Can you elaborate what you have done and what is not working ? You typically install tool repositories into Galaxy. The things that start with package_ are deprecated and will not show up in any search by default in the upcoming 20.01 release.
Thanks for replying.
So far, I’ve been asked to look at a few issues including an existing Prokka installation that didn’t work–which I fixed when I realized it’s basically just a conda environment so I just manually reinstalled the environment using conda.
Assemblystats, which turned out assumed gnuplot is always present: so I manually installed this, then edited the perl script to update $PATH. In this instance I can see many packages have a location under under ‘database/dependencies’ where often there is is an env.sh, though not in the case of Assemblystats (just wondering if there is a way to tweak an installation to make these kinds of changes).
At the moment I’m going round in circles over a gatk installation (from toolshed.g2.bx.psu.edu, avowinkel, b80ff7f43ad1). It’s listed as ‘Installed, missing tool dependencies’–seem to be problem with package_r_for_gatk_3_4_0, which seem to have some issue with R 3.1.2. When I tried to ‘Activate or reinstall repository’ via the ‘Repository Actions’ button, all I get after a long-ish delay is the message ‘There is no repository being installed’.
Hence I wish to get a better understanding about how the process works under the hood.
Regards
Michael
Good to know about the deprecated package_. In general our users are just asking for what they already knows (I probably know rather less than them).
Michael